Complexity Digest 2009.10

2009/05/08

Editor-in-Chief: Carlos Gershenson
Founding Editor: Gottfried Mayer

Contributing Editors Wanted
Interested members of the complexity community, please send an e-mail to editor@comdig.org . The role of contributing editors is to monitor potential sources of material for ComDig and submit content for its inclusion in ComDig issues.

Out of Mexico? Scientists Ponder Swine Flu's Origins, Science

How severe will the flu outbreak be?, Nature News

Devilish Dilemmas Surround Pandemic Flu Vaccine, Science

What can we learn from the 1918 flu pandemic?, TED.com

The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics, PLoS Comput Biol

A Dynamic Network Approach for the Study of Human Phenotypes, PLoS Comput Biol

Cloud Computing: A New Horizon, ScienceDaily

Rousing a Latent Defense Mechanism to Fight HIV, PLoS Biol

Ten Simple Rules To Combine Teaching and Research, PLoS Comput Biol

The reductionist blind spot, Complexity

On irreducible description of complex systems, Complexity

A Brief History of Information-Based Complexity, SFI Working Papers

Climate change: Too much of a bad thing, Nature

The worst-case scenario, Nature

Chemistry: Fuel from thin air, Nature

Climate: Ground truths, Nature

What's Bugging Plants?, Science

Why Stock-price Volatility Should Never Be a Surprise, Even in the Long Run, Knowledge@Wharton

Summary: The origin of the virus behind the current swine flu outbreak, its muscle power, and how much of a threat it presents remain mysteries. After Mexico, the United States has had the most cases, which on 5 May totaled 403. The almost simultaneous confirmations of the outbreak in both Mexico and the United States initially added further confusion to the outbreak's origins. But the virus itself has helped clear up some matters. The greatest concern is what will this confusing virus, which combines genes from swine, avian, and human influenza strains, do next?See Also:Science Insider reports on the Swine Flu.

Excerpt: "My own personal view is that it is too early to say what the severity is," says Lipsitch, (...). One reason the disease appears mild is that in the United States there has been only one reported death among 286 cases. But such case-fatality rates, reported one week after a case is confirmed, can underestimate actual mortality rates, because they can overlook patients who remain ill and subsequently die. This was demonstrated in 2003, when the reported case-fatality rate of severe acute respiratory syndrome (SARS) in Asia was initially put at a few per cent â€" only to be found to be closer to 20% in studies that followed up cases.

Summary: If and when a pandemic of H1N1 swine flu hits, vaccines might be the world's best hope for softening the blow. But major uncertainties cloud the prospects for vaccines against the new strain. No pandemic vaccine yet exists, and it is unclear how much vaccine would have to be available, and by what time, to have any impact. Should manufacturers halt the production of seasonal influenza vaccine to focus on a pandemic version, and if so, when? And is there any way to ensure that people around the world have an equal chance to get the new vaccine?

About this talk: In 2007, as the world worried about a possible avian flu epidemic, Laurie Garrett, author of "The Coming Plague," gave this powerful talk to a small TED University audience. Her insights from past pandemics are suddenly more relevant than ever.

Source: What can we learn from the 1918 flu pandemic?[ http://www.ted.com/index.php/talks/laurie_garrett_on_lessons_from_the_1918_flu.html ], Laurie Garrett, TED.com, 2009/04

The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics, PLoS Comput Biol

Excerpt: Avian influenza virus (AIV) persists in North American wild waterfowl, exhibiting major outbreaks every 2â€"4 years. Attempts to explain the patterns of periodicity and persistence using simple direct transmission models are unsuccessful. Motivated by empirical evidence, we examine the contribution of an overlooked AIV transmission mode: environmental transmission. It is known that infectious birds shed large concentrations of virions in the environment, where virions may persist for a long time. We thus propose that, in addition to direct fecal/oral transmission, birds may become infected by ingesting virions that have long persisted in the environment.

Excerpt: The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing correlations obtained from the disease history of more than 30 million patients in a Phenotypic Disease Network (PDN). We present evidence that the structure of the PDN is relevant to the understanding of illness progression by showing that (1) patients develop diseases close in the network to those they already have; (2) the progression of disease along the links of the network is different for patients of different genders and ethnicities; (3) patients diagnosed with diseases which are more highly connected in the PDN tend to die sooner than those affected by less connected diseases; and (4) diseases that tend to be preceded by others in the PDN tend to be more connected than diseases that precede other illnesses, and are associated with higher degrees of mortality.

Excerpt: The outlook is bleak for laptops, hard drives and desktops - clouds are on the horizon and could change the way we use computers forever. For some, the ‘cloud' is just the latest technological craze, but for others it is the future of computing, and it has already generated a large body of research literature. What seems certain is that cloud computing has the potential to bring about irreversible changes in the way computers are used around the world. (...)

Excerpts: Venkataraman et al. focused their work on retrocyclin, a member of the defensin family of proteins. Defensins are made by all primates and have potent anti-microbial activity. Retrocyclin was recently shown to strongly inhibit HIV entry into human cells by blocking the interaction of viral proteins with their cellular receptors. Unfortunately, although the retrocyclin protein is found in Old World monkeys and orangutans, it is not present in humans (or gorillas and chimps), even though we have the retrocyclin gene. (...) Collectively, these results suggest that human cells have a potentially importantâ€"but latentâ€"mechanism to protect against HIV.

Excerpt: The late Lindley J. Stiles famously made himself an advocate for teaching during his professorship at the University of Colorado: â€śIf a better world is your aim, all must agree: The best should teachâ€ť (http://thebestshouldteach.org/ ). In fact, dispensing high-quality teaching and professional education is the primary goal of any university. Thus, for most faculty positions in academia, teaching is a significant requirement of the job. Yet, the higher education programs offered to Ph.D. students do not necessarily incorporate any form of teaching exposure. We offer 10 simple rules that should help you to get prepared for the challenge of teaching while keeping some composure.

Abstract: Can there be higher level laws of nature even though everything is reducible to the fundamental laws of physics? The computer science notion of level of abstraction explains how there can be. The key relationship between elements on different levels of abstraction is not the is-composed-of relationship but the implements relationship. I take a scientific realist position with respect to (material) levels of abstraction and their instantiation as (material) entities. They exist as objective elements of nature. Reducing them away to lower order phenomena produces a reductionist blind spot and is bad science.

Abstract: The aim of the article is to present the description of complex systems in terms of self-organization processes of prime integer relations and illustrate its main properties. Based on the integers and controlled by arithmetic only, the processes can characterize complex systems by information not requiring further simplification. This raises the possibility to develop an irreducible theory of complex systems.

Abstract: The goal of information-based complexity is to create a theory of optimal algorithms and computational complexity for problems with partial, contaminated and priced information, and to apply the results to solving specific problems in various disciplines. The continuous mathematical models which occur in the physical and social sciences and engineering typically have only partial, contaminated, and priced information. Such problems usually have to be solved numerically to within a certain error threshold. Of particular interest are problems in hundreds or thousands of variables. A central issue is vanquishing the resulting "curse of dimensionality." Information-based complexity has been applied to fields ranging from computational finance to quantum computing. This paper traces the history of information-based complexity to the present.

The black line shows the probability of the peak global mean temperature exceeding 2 Â°C above pre-industrial levels before the year 2100 as a function of the integrated emissions from 2009 to 2049. (...)

There are various â€" and confusing â€" targets to limit global warming due to emissions of greenhouse gases. Estimates based on the total slug of carbon emitted are possibly the most robust, and are worrisome.See Also:The Climate Crunch online collection.

Excerpt: In a 1,000 p.p.m. scenario, many unique or rare systems would probably be lost, including Arctic sea ice, mountain-top glaciers, most threatened and endangered species, coral-reef communities, and many high-latitude and high-altitude indigenous human cultures. People would be vulnerable in other ways too: Asian mega-delta cities would face rising sea levels and rapidly intensifying tropical cyclones, creating hundreds of millions of refugees; valuable infrastructure such as the London or New York underground systems could be damaged or lost; the elderly would be at risk from unprecedented heat waves; and children, who are especially vulnerable to malnutrition in poor areas, would face food shortages.

Excerpt: Carbon dioxide can be sucked out of the air (...) and turned into a useful fuel using a metal-free catalyst. The carbene catalyst â€" a compound with a pair of electrons available to react â€" is not only metal-free, and so better for the environment, it also works in air. Metal catalysts are often degraded by oxygen.See Also:Angew. Chem. Int. Edn 48, 3322â€"3325 (2009)

Excerpt: Clive McAlpine of the University of Queensland in Australia and his colleagues simulated the period from 1951 to 2003 on computer climate models â€" comparing actual land use change with a scenario in which land stayed in its late-eighteenth-century pre-European state. The results imply that clearing native vegetation has worsened droughts, even if climate change is factored out.See Also:Geophys. Res. Lett. doi:10.1029/2009GL037666 (2009)

Excerpt: Plants, like other organisms, including animals, live immersed in a thriving community of microbes. The diversity of fungi, oomycetes, and bacteria with which plants interact brings both plague and benefit. The more we understand how plants tame, thwart, and succumb to their bugs, the more likely we will be able to extract new resources for antimicrobial treatments and manage agricultural challenges

Why Stock-price Volatility Should Never Be a Surprise, Even in the Long Run, Knowledge@Wharton

Summary: Stock market investors have suffered deep losses in the past 18 months, challenging the belief that stocks are the best long-term investments. Indeed, Wharton finance and economics professor Robert Stambaugh recently coauthored a paper titled, "Are Stocks Really Less Volatile in the Long Run?," which suggests that equities are subject to bigger price swings than previously understood. The research adds a new perspective to the work of Wharton finance professor Jeremy J. Siegel, author of the book, Stocks for the Long Run, which says stock returns more than offset risks if you stay with the market through its ups and downs. In a recent interview with Knowledge@Wharton, the professors described their views about the market's long-term behavior.

Source: Why Stock-price Volatility Should Never Be a Surprise, Even in the Long Run[ http://knowledge.wharton.upenn.edu/article.cfm?articleid=2229 ], Knowledge@Wharton, 2009/04/29

Abstract: Optimization has been shown to be a driving force for the evolution of some biological structures, such as neural maps in the brain or transport networks. Here we show that insect networks also display characteristic traits of optimality. By using a graph representation of the chamber organization of termite nests and a disordered lattice model, it is found that these spatial nests are close to a percolation threshold. This suggests that termites build efficient systems of galleries spanning most of the nest volume at low cost. The evolutionary consequences are outlined.

Abstract: The promotion of cooperation on spatial lattices is an important issue in evolutionary game theory. This effect clearly depends on the update rule: it diminishes with stochastic imitative rules whereas it increases with unconditional imitation. To study the transition between both regimes, we propose a new evolutionary rule, which stochastically combines unconditional imitation with another imitative rule. We find that, surprinsingly, in many social dilemmas this rule yields higher cooperative levels than any of the two original ones. This nontrivial effect occurs because the basic rules induce a separation of timescales in the microscopic processes at cluster interfaces. The result is robust in the space of 2x2 symmetric games, on regular lattices and on scale-free networks.

Excerpt: In the world of genome repair analysis, much attention has been focused on the mechanism underlying error-free repair of DNA double-strand breaks. This process, which involves homologous recombinationâ€" based repair, warrants close attention, not least because failure to repair double-strand breaks can be lethal. Similarly, disorderly repair can result in loss of chromosomal integrity and spur tumor development. Three recent studies emphasize the complex nature of the suspected link between the homologous recombination mechanism in mammalian cells and the suppression of cancer.

Excerpts: A Duke University professor and his graduate student have discovered a universal principle that unites the curious interplay of light and shadow on the surface of your morning coffee with the way gravity magnifies and distorts light from distant galaxies. They think scientists will be able to use violations of this principle to map unseen clumps of dark matter in the universe. Light rays naturally reflect off a curve like the inside surface of a coffee cup in a curving, ivy leaf pattern that comes to a point in the center and is brightest along its edge. (...)

Excerpt: As scientists are celebrating the 200th anniversary of Charles Darwin's birth and the 150th anniversary of the publication of his On the Origin of Species, Darwin's ideas continue to shape and enrich the sciences. 6 May 2009 marks the 150th anniversary of the death of another 19th-century figureâ€"Alexander von Humboldtâ€"whose scientific legacy also flourishes in the 21st century. Humboldt helped create the intellectual world Darwin inhabited, and his writings inspired Darwin to embark on H.M.S. Beagle. More pertinent to our time, Humboldt established the foundation for the Earth system sciences: the integrated system of knowledge on which human society may depend in the face of global climate change.

'The Two Cultures' was the title of Snow's hugely influential Rede Lecture at the University of Cambridge, UK, on 7 May 1959. One culture was science; the other was the humanities, as represented by "literary intellectuals". Snow decried what he saw as the total inability of highly educated people to cross a deep rift of mutual incomprehension.

Excerpts: Of all the features of autism, none is more widely admired than the remarkable talent found so frequently with this condition. Yet special talents are still less researched and less well understood than other features of autism. In popular accounts of autism, the existence of extraordinary talent in art, music, maths, calendar calculation or memory, often referred to as savant skills, has become a stock in trade. As a result of this fascination, it is now very likely that any eccentric scientist or artist, living or dead, will come under scrutiny (...). But are geniuses, such as Newton or Einstein, personifications of the association of autism and talent? (...)

Excerpt: Outsider Art (art brut) is defined as a mode of original artistic expression which thrives on its independence, shunning the public sphere and the art market. Such art can be highly idiosyncratic and secretive, and reflects the individual creator's attempt to construct a coherent, albeit strange, private world. Certain practitioners of what may be termed autistic art are examined in the light of this definition; their work is considered as evidence not of a medical condition but of an expressive intentionality entirely worthy of the interest of those drawn to the aesthetic experience. (...)

How Does Visual Thinking Work In The Mind Of A Person With Autism? A Personal Account, Phil. Tran. Biol. Sc.

Excerpt: My mind is similar to an Internet search engine that searches for photographs. I use language to narrate the photo-realistic pictures that pop up in my imagination. When I design equipment for the cattle industry, I can test run it in my imagination similar to a virtual reality computer program. All my thinking is associative and not linear. To form concepts, I sort pictures into categories similar to computer files. To form the concept of orange, I see many different orange objects, such as oranges, pumpkins, orange juice and marmalade. (...)

Source: How Does Visual Thinking Work In The Mind Of A Person With Autism? A Personal Account[ http://rstb.royalsocietypublishing.org/content/364/1522/1437.abstract ], T. Grandin - cheryl.millercolostate.edu, DOI: 10.1098/rstb.2008.0297, Philosophical Transactions: Biological Sciences, May 2009

Abstract: Based on the stability analysis of the impulsive functional differential equation, the exponential synchronization of the complex dynamical network with a coupling delay and impulses is investigated in the paper. The criteria for the exponential synchronization are derived by the geometrical decomposition of network states and linear matrix inequality method. Two examples are given to show the effectiveness of the proposed criteria.

Excerpt: How do Chinese consumers really feel about Western brands? We often hear that magazines and billboards influence Chinese consumers to imitate Western lifestyles. Meanwhile, Chinese "patriots" are thought to reject Western brands as a symbolic gesture of loyalty to their country. A new study in the Journal of Consumer Research paints a more complex picture. In a series of surveys and in-depth interviews with Chinese consumers in rural and urban areas, the authors found that Chinese consumers attach political meanings to Western brands and connect those brands to important moments in Chinese history, like Mao Zedong's Cultural Revolution or Deng Xiaoping's economic reforms. (...)

Other Announcements

Postdoc positions: The New England Complex Systems Institute (NECSI) has openings for postdoctoral appointments in the study of complex systems. In addition to general projects, there will be openings in research fields such as: Social and global systems, biological systems, cognitive systems, evolution, non-equilibrium dynamics, agent based modeling, multiscale analysis, complex systems engineering, management/organization science, and education of complex systems concepts. Postdocs should have experience with modeling techniques and computer simulation, data analysis, and/or analytic skills. The ideal candidate will also have strong writing abilities and a desire to work in diverse fields. A commitment to larger social concerns is highly desirable, as NECSI research informs policy in areas such as the national and global economy, health care, the environment and ecology. NECSI Postdoctoral fellows may also receive joint appointments at MIT, Harvard, or other Boston-area academic institutions. For more information and directions on submitting applications, please visit: http://necsi.edu/education/postdoc.html

Postdoc positions: The C3 - Centro de Ciencias de la Complejidad, a new interdisciplinary, inter-institutional research center based at the Universidad Nacional Autonoma de Mexico (UNAM) plans to have several openings for postdoctoral candidates in the coming months. The center currently has affiliated to it more than 50 researchers and 40 students from all the major scientific disciplines. The main research topics at the moment are: Genetic networks and Systems Biology, Ecological Complexity, Social Complexity and Computational Intelligence. Salary will be in the region of 20-25,000 pesos per month. Interested candidates are asked to send a CV, a statement of research interests and the names of at least three potential referees to: Dr. Chris Stephens (Ecological Complexity and Computational Intelligence) stephens@nucleares.unam.mx Dra. Elena Alvarez-Buylla (Systems Biology) eabuylla@gmail.com Dr. Gustavo Martinez-Mekler (Social Complexity and other areas) mekler@ce.fis.unam.mx

New Book: Complexity: A Guided Tour, by Melanie Mitchell. Oxford University Press, 2009. What enables individually simple insects like ants to act with such precision and purpose as a group? How do trillions of individual neurons produce something as extraordinarily complex as consciousness? What is it that guides self-organizing structures like the immune system, the World Wide Web, the global economy, and the human genome? These are just a few of the fascinating and elusive questions that the science of complexity seeks to answer. In this remarkably accessible and companionable book, leading complex systems scientist Melanie Mitchell provides an intimate, detailed tour of the sciences of complexity, a broad set of efforts that seek to explain how large-scale complex, organized, and adaptive behavior can emerge from simple interactions among myriad individuals. Comprehending such systems requires a wholly new approach, one that goes beyond traditional scientific reductionism and that re-maps long-standing disciplinary boundaries. Based on her work at the Santa Fe Institute and drawing on its interdisciplinary strategies, Mitchell brings clarity to the workings of complexity across a broad range of biological, technological, and social phenomena, seeking out the general principles or laws that apply to all of them. She explores as well the relationship between complexity and evolution, artificial intelligence, computation, genetics, information processing, and many other fields. Richly illustrated and vividly written, Complexity: A Guided Tour offers a comprehensive and eminently comprehensible overview of the ideas underlying complex systems science, the current research at the forefront of this field, and the prospects for the field's contribution to solving some of the most important scientific questions of our time.